Use of unphased multilocus genotype data in indirect association studies

Clayton, David; Chapman, Juliet; Cooper, Jason

doi:10.1002/gepi.20032

Cited by 186Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsForensic and Genetic Research

Use of unphased multilocus genotype data in indirect association studies

Clayton, David, Chapman, Juliet, Cooper, Jason·2004·Genetic Epidemiology

DOI 10.1002/gepi.20032

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Abstract

It is usually assumed that detection of a disease susceptability gene via marker polymorphisms in linkage disequilibrium with it is facilitated by consideration of marker haplotypes. However, capture of the marker haplotype information requires resolution of gametic phase, and this must usually be inferred statistically. Recently, we questioned the value of the marker haplotype information, and suggested that certain analyses of multivariate marker data, not based on haplotypes explicitly and not requiring resolution of gametic phase, are often more powerful than analyses based on haplotypes. Here, we review this work and assess more carefully the situations in which our conclusions might apply. We also relate these analyses to alternative approaches to haplotype analysis, namely those based on haplotype similarity and those inspired by cladistics. © 2004 Wiley‐Liss, Inc.

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Approaches that capture subtle synergistic effects among many loci in a region, or among different variant types affecting gene function, such as sequence- or functional-similarity-based methods, are probably also suitable.
“However, methods which can account for subtle synergistic effects of many loci within a defined region and/or different forms of variation that might contribute to gene function, such as those rooted in sequence or functional similarity56, 57, 87, 88 are also likely to be appropriate.”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [56]

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INSTITUTE OF STATISTICS MIMEO SERIES #2606 Regression-based Multi-marker Analysis for Genome-wide Association Studies Using Haplotype Similarity
Tzeng, J., Chang, S.-M., Zhang, D., Thomas, D., & Davidian, M. (2008)
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Authors: Clayton, D., Chapman, J., & Cooper, J.
Affiliations: University of Cambridge (GB)
Corresponding author: Clayton, David
ORCID: Clayton, David
Cooper, Jason
Venue: Genetic Epidemiology
Publisher: Wiley
Published: 2004-10-12
Volume: 27
Issue: 4
Pages: 415-428
ISSN: 0741-0395 (ISSN-L)
1098-2272
DOI: 10.1002/gepi.20032
OpenAlex: W2029784047
Cited by: 186
References: 33
Citations by year: 2025: 3 · 2023: 2 · 2022: 1 · 2019: 1 · 2018: 2 · 2016: 4 · 2015: 4 · 2014: 4 · 2013: 5 · 2012: 3
FWCI: 15.66
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Genetic Epidemiology (publishedVersion)
PubMed (publishedVersion)
LSHTM Research Online (London School of Hygiene and Tropical Medicine) (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords: linkage disequilibrium, susceptibility genes
MeSH terms: Genetic Markers, Genetics, Population, Genotype, Haplotypes, Humans, Models, Genetic, Models, Statistical, Linkage Disequilibrium, Genetic Predisposition to Disease

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Use of unphased multilocus genotype data in indirect association studies

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